Background: There is a pressing need for policy makers to demonstrate progress made on investments in prevention, but few examples of monitoring systems capable of tracking population-level prevention policies and programs and their implementation. In New South Wales, Australia, the scale up of childhood obesity prevention programs to over 6000 childcare centres and primary schools is monitored via an electronic monitoring system, "PHIMS". Methods: Via a focussed ethnography with all 14 health promotion implementation teams in the state, we set out to explore what aspects of program implementation are captured via PHIMS, what aspects are not, and the implications for future IT implementation monitoring systems as a result. Results: Practitioners perform a range of activities in the context of delivering obesity prevention programs, but only specific activities are captured via PHIMS. PHIMS thereby defines and standardises certain activities, while non-captured activities can be considered as "extra"work by practitioners. The achievement of implementation targets is influenced by multi-level contextual factors, with only some of the factors accounted for in PHIMS. This evidences incongruencies between work done, recorded and, therefore, recognised. Conclusions: While monitoring systems cannot and should not capture every aspect of implementation, better accounting for aspects of context and "extra"work involved in program implementation could help illuminate why implementation succeeds or fails. Failure to do so may result in policy makers drawing false conclusions about what is required to achieve implementation targets. Practitioners, as experts of context, are well placed to assist policy makers to develop accurate and meaningful implementation targets and approaches to monitoring.